Solid-state integrated real-time optical monitoring of biochemical assays

ABSTRACT

The disclosed technology includes a planar device for performing multiple biochemical assays at the same time, or nearly the same time. Each assay may include a biosample including a biochemical, enzyme, DNA, and/or any other biochemical or biological sample. Each assay may include one or more tags including dyes and/or other chemicals/reagents whose optical characteristics change based on chemical characteristics of the biological sample being tested. Each assay may be optically pumped to cause one or more of luminescence, phosphorescence, or fluorescence of the assay that may be detected by one or more optical detectors. For example, an assay may include two tags and a biosample. Each tag may be pumped by different wavelengths of light and may produce different wavelengths of light that is filtered and detected by one or more detectors. The pump wavelengths may be different from one another and different from the produced wavelengths.

FEDERALLY SPONSORED RESEARCH OR DEVELOPMENT

The United States Government has rights in this invention pursuant toContract No. DE-AC52-07NA27344 between the U.S. Department of Energy andLawrence Livermore National Security, LLC, for the operation of LawrenceLivermore National Laboratory.

TECHNICAL FIELD

The present disclosure relates to monitoring biochemical assays.

BACKGROUND

Multiple biological and/or biochemical tests may be performed forpatient diagnosis and treatment. Each test may require one or moredifferent reagents, enzymes, or biosamples. The multiple tests may beconducted individually in serial with one test being performed afteranother, or in parallel with multiple tests being performed at the sametime. The multiple tests may require different materials such asdifferent reagents, different biosamples, and different test excitationssuch as different light sources. Some may require heating of biosamples,the reagents, and/or enzymes. Techniques and equipment are needed toreduce the size of equipment required to run multiple tests, reduce thecosts, and to increase the speed of testing.

SUMMARY

In one aspect, an apparatus such as a planar biochemical device isdisclosed. The device includes a plurality of sample holders arranged ina planar configuration forming a one-dimensional or a two-dimensionalarray, each sample holder configured for an assay comprising one or morebiosamples and one or more reagents, a planar heater coupled to theplurality of sample holders, wherein the planar heater is operable toheat the plurality of sample holders, an optical substrate layer coupledto the planar heater, wherein the optical substrate layer distributeslight from one or more optical sources to each of the sample holders,and an optical detection layer positioned to receive light from theplurality of sample holders, the optical detection layer including oneor more optical detectors in alignment with each sample holder to detectlight corresponding to each assay.

The planar biochemical device can include any of the following featuresin any combination. The planar biochemical device can include one ormore optical filters positioned between the optical detection layer andthe optical substrate, wherein each optical filter passes light of apredetermined wavelength and bandwidth and rejects light outside thepredetermined wavelength and bandwidth. The planar biochemical devicecan include one or more diffraction gratings positioned between theoptical detection layer and the optical substrate, the diffractiongratings separate different colors in the received light with little orno attenuation, and wherein the optical detection layer includes atwo-dimensional array of charge-coupled optical detectors, or atwo-dimensional array of complementary metal oxide semiconductor opticaldetectors. The optical substrate layer includes a source fiber withoutcouplers at locations corresponding to each of the sample holders.The one or more biosamples and the one or more reagents are related to apolymerase chain reaction. The one or more optical sources produce lightcentered at at least two different wavelengths. The received lightincludes luminescent light resulting from a chemical reaction in a firstassay. The received light includes fluorescent light resulting fromexcitation of a sample in a first assay. The received light includesphosphorescent light resulting from excitation of a sample in a firstassay. The optical substrate layer is configured to receive light fromthe one or more optical sources through an optical fiber. The opticalsubstrate layer is configured by machining or etching to accept, align,and/or self-register one or more lenses associated with the one or morebiosamples. Light from the optical fiber is coupled to one or more ofthe plurality of sample holders through openings in the optical fibercladding, where this cladding is removed at a plurality of predeterminedlocations. The openings in the optical fiber cladding have differentsizes at at least two of the plurality of predetermined locations toallow different amounts light to be emitted towards at least two of thesample holders.

In another aspect, a method of processing a plurality of biosamples isdisclosed. The method includes providing, in a first sample holder of aplanar biosample monitoring device, a biosample and one or morereagents, wherein the first sample holder is one of a plurality ofsample holders, wherein each sample holder includes a different assay,heating the plurality of sample holders by a planar heater coupled tothe plurality of sample holders, distributing, by an optical substratelayer coupled to the plurality of sample holders, light from one or moreoptical sources to provide excitation of the different assays,filtering, by one or more filters coupled to the substrate layer, lightgenerated by the one or more reagents in response to the excitation, anddetecting, by one or more detectors coupled to the one or more filters,light emitted from the plurality of assays, wherein each of thedifferent assays in the plurality of sample holders emits light that isdetected by one or more different detectors coupled to the one or morefilters.

The following features may be included in any combination. The opticalsubstrate layer includes a source fiber with outcouplers at locationscorresponding to each of the sample holders. The biosample and the oneor more reagents are related to a polymerase chain reaction. The emittedlight includes luminescent light resulting from a chemical reaction. Theemitted light includes fluorescent light resulting from excitation of asample in a first assay. The emitted light includes phosphorescent lightresulting from excitation of a sample in a first assay.

In yet another aspect a planar biochemical apparatus is disclosed. Theapparatus includes one or more sample holders including a first sampleholder, wherein each sample holder includes an assay with one or morebiosamples and one or more reagents, wherein the first sample holderincludes a first assay, a planar heater to heat the one or more sampleholders, and a planar optical assembly comprising: one or more opticalsources to provide excitation to the first assay; and one or moredetectors to detect light emitted from the first assay.

In yet another aspect, another planar biochemical device is disclosed.The device includes a plurality of sample holders arranged in a planarconfiguration forming a one-dimensional array, each sample holderconfigured for an assay comprising one or more biosamples and one ormore reagents, a planar heater coupled to the plurality of sampleholders, wherein the planar heater is operable to heat the plurality ofsample holders, an optical substrate layer coupled to the planar heater,wherein the optical substrate layer distributes light from one or moreoptical sources to each of the sample holders, a filter layer comprisingtwo or more filters positioned to receive light from the plurality ofsample holders, wherein the optical substrate layer causes the receivedlight from each sample holder to fall on two filters, wherein eachfilter is positioned to receive light from two sample holders throughthe optical substrate, and an optical detection layer positioned toreceive light from the filter layer, the optical detection layerincluding two optical detectors per sample holder, wherein the twooptical detectors are positioned to receive the light from the twofilters associated with each assay.

The apparatus may include a plurality of sample holders including afirst sample holder. Each sample holder may perform a different assay onone or more biosamples and one or more reagents, wherein the firstsample holder performs a first assay. The apparatus may further includea planar heater coupled to the plurality of sample holders, wherein theplanar heater heats the plurality of sample holders. The apparatus mayinclude an optical substrate layer coupled to the planar heater. Theoptical substrate layer may distribute one or more optical sources toprovide excitation to the different assays including the first assay.The apparatus may further include an optical detection layer coupled tothe optical substrate layer. The optical detection layer may include oneor more optical detectors per sample holder to detect light emitted fromeach assay. At least one of the optical detectors may detect lightemitted from the first assay in the first sample holder. A first filtermay be configured to receive light from a first sample holder, wherein afirst detector from the one or more detectors is configured to receivelight from the first filter. A second filter may be configured toreceive light from the first sample holder, wherein a second detectorfrom the one or more detectors is configured to receive light from thesecond filter

In another aspect, a method of processing a plurality of biosamples isdisclosed. The method may include containing, in a first sample holder,a biosample and one or more reagents. The first sample holder may be oneof a plurality of sample holders and the first sample holder may includea first assay. Each sample holder may include a different assay. Themethod may further include heating the plurality of sample holders by aplanar heater coupled to the plurality of sample holders. The method mayinclude distributing, by an optical substrate layer coupled to theplurality of sample holders, one or more optical sources to provideexcitation of the different assays including the first assay. The methodmay further include filtering, by one or more filters coupled to thesubstrate layer, light generated by the one or more reagents in responseto the excitation. The method may include detecting, by one or moredetectors coupled to the one or more filters, light emitted from thefirst assay. Each of the different assays in the plurality of sampleholders may emit light that is detected by one or more differentdetectors coupled to the one or more filters.

In another aspect, a planar biochemical apparatus is disclosed. Theapparatus may include one or more sample holders including a firstsample holder. Each sample holder may include an assay with one or morebiosamples and one or more reagents. The first sample holder may includea first assay. The apparatus may further include a planar heater to heatthe one or more sample holders. The apparatus may include a planaroptical assembly. The planar optical assembly may include one or moreoptical sources to provide excitation to the first assay. The planaroptical assembly may further include one or more detectors to detectlight emitted from the first assay.

The following features may be included in any combination. One or moreoptical filters may be included between the optical detection layer andthe optical substrate, wherein the optical detection layer includes anarray of photodetectors. One or more diffraction gratings may beincluded between the optical detection layer and the optical substrate,wherein the optical detection layer includes a two-dimensional array ofcharge-coupled optical detectors, or another two-dimensional array ofcomplementary metal oxide semiconductor optical detectors. The opticalsubstrate layer may include a source fiber with outcouplers at locationscorresponding to each of the sample holders. The one or more biosamplesand the one or more reagents may be related to a polymerase chainreaction. The planar heater may accelerate a polymerase chain reaction.The emitted light may include luminescent light, fluorescent light,and/or phosphorescent light resulting from a chemical reaction in thefirst assay. Light from the one or more optical sources may propagate inan optical fiber. The optical fiber may be attached to the opticalsubstrate. Cladding around the optical fiber may be removed at aplurality of predetermined locations to cause light emission at thepredetermined locations, wherein the light emission causes excitation ofthe assays. Different amounts of the cladding may be removed at theplurality of predetermined locations to cause the light emission fromeach of the predetermined locations to be approximately equal inintensity.

The above and other aspects of the disclosed technology are described ingreater detail in the drawings, the description and the claims.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 depicts an example of a bioassay system, in accordance with someexample embodiments;

FIG. 2 depicts another example of a bioassay system, in accordance withsome example embodiments;

FIG. 3 depicts an example of combining multiple optical sources andexamples of outcouplers, in accordance with some example embodiments;

FIG. 4 depicts an example of collection optics, in accordance with someexample embodiments;

FIG. 5 depicts an example of a plot of wavelength vs. optical densityfor an example optical filter, in accordance with some exampleembodiments;

FIG. 6 depicts an example of bioassays with two optical filters and twodetectors per bioassay, in accordance with some example embodiments;

FIG. 7 depicts an example of parameter values for various dyes using adiffraction grating with 1200 lines per millimeter, in accordance withsome example embodiments; and

FIG. 8 depicts an example of a process, in accordance with some exampleembodiments.

DETAILED DESCRIPTION

The disclosed technology includes a planar device for performingmultiple biochemical assays at the same time, or nearly the same time.Each assay may include a biosample including a biochemical, enzyme, DNA,and/or any other biochemical or biological sample. Each assay mayinclude one or more tags including dyes and/or other chemicals/reagentswhose optical characteristics change based on chemical characteristicsof the biological sample being tested. Each assay may be opticallypumped to cause one or more of luminescence, phosphorescence, orfluorescence of the assay that may be detected by one or more opticaldetectors. For example, an assay may include two tags and a biosample.Each tag may be pumped by different wavelengths of light and may producedifferent wavelengths of light that are filtered and detected by one ormore detectors. The pump wavelengths may be different from one anotherand different from the produced wavelengths. The planar apparatus may becompact in size and suitable for a hand held, hand carried, or smallerbioassay system.

The optical characterization of tags in a sample well (also referred toas a sample holder) may require optical pumping with one or morepredetermined wavelengths, and collection of the light emitted from thetags including light generated by luminescence, phosphorescence, and/orfluorescence. The intensities of one or more wavelengths in thecollected light may be determined. The apparatus may include a planarintegrated optical system for bringing excitation or observation lightinto the sample wells and extracting, filtering, and detecting theemitted light. Multiple sample wells may be combined into the planarapparatus and each sample well may be interrogated at the same time, ornearly the same time, while maintaining a small form factor usinginexpensive and manufacturable devices. Simultaneous interrogation ornearly simultaneous interrogation of two or more different tags may beperformed by pumping the biosample and tags with multiple wavelengthsand filtering the multiple wavelengths before being detected by one ormore optical detectors.

FIG. 1 depicts an example of a bioassay system 100, in accordance withsome example embodiments. In the example of FIG. 1, the bioassay systemincludes sample wells (or holders) 110A-110C, thermal layer 130,illuminators 114A-114C, optical source(s) 140, optical splitter 120,collection optics 112A-112C, filters 170A-170C, and detectors 160A-160Cto detect fluorescent light, luminescent light, and/or phosphorescentlight from one or more tags.

In the example of FIG. 1, each of the sample wells 110A, 110B, and 110Cmay hold one of more biosamples and/or one or more tags. The differentsample wells may hold the same biosample or different biosamples. Thedifferent sample wells may include the same tags or different tags. Forexample, sample well 110A may include a first biosample and aphosphorescent tag, sample well 110B may include the first biosample anda luminescent tag and a fluorescent tag, and sample well 110C mayinclude a second biosample and a phosphorescent tag, a luminescent tag,and a fluorescent tag. Although three sample wells, 110A, 110B, and 110Care shown in the example of FIG. 1, the bioassay system 100 may includeany other number of sample wells, any number of biosamples, and anynumber of tags. The biosample wells of bioassay system 100 may bearranged in a one dimensional or a two-dimensional array configuration.For example, the bioassays may be arranged in a one-dimensional array of10 sample wells in a row, or a two-dimensional array of six assays bysix assays for a total of 36 assays.

Sample wells 110A-110C may be heated (or cooled) by thermal layer 130.For example, heating layer 130 may be in direct contact, or nearly indirect contact with sample wells 110A-110C. Heating by the thermal layermay accelerate a polymerase chain reaction (PCR) reaction in one or moreof the sample wells 110A-110C. The thermal layer may be planar and mayhave a copper, aluminum, silicon, or other material aligned with thesample wells 110A-110C.

Illuminators 114A-114C may provide light to pump the biosamples and tagsin sample wells 110A-110C. Optical splitter 120 may distribute lightfrom optical source(s) 140 to illuminators 114A-114C. Optical source(s)140 may provide light to optical splitter 120 via one or more opticalfibers 142 (also referred to herein as source fiber 142). For example,optical source(s) 140 may include two optical sources that produce lightof different wavelengths. Light form both sources may be combined andpassed from 140 to optical splitter 120. Optical source(s) 140 may beswitched on and off and/or the drive current adjusted as a function oftime by controller 150. In the example of FIG. 1, optical splitter 120may split the light passed along fiber 142 into three parts; one partfor each illuminator 114A-114C. Optical splitter 120 may pass light ofone or both wavelengths to each illuminator. For example, opticalsplitter 120 may pass a portion of the optical power at two wavelengthsto illuminator 114A, a portion of the optical power of one wavelength toilluminator 114B, and a portion of the optical power of the otherwavelength to illuminator 114C. Any other combination of wavelengths maybe passed to each illuminator. Illuminators 114A-114C may causecolumniation of the emitted light into the bioassays. In some exampleembodiments, optical splitter 120 and/or illuminators 114A-114C mayinclude optical filters to select the wavelength(s) of light that arethe sample wells. In some example embodiments, splitter 120 andilluminators 114A-114C may be combined. For example, optical splittingmay be performed by optical fiber 142 with the cladding of the opticalfiber removed at locations corresponding to sample wells 110A-110C.Different amounts of cladding may be removed at the different locationsof the sample wells 110A-110C to cause the optical power emitted at eachof the sample wells to be equal or nearly equal.

Illumination of the bioassays and tags by illuminators 114A-114C causethe tags to luminesce, fluoresce, and/or phosphoresce. The luminescentlight, fluorescent light, and/or phosphorescent light may be collectedby collection optics 112A-112C, passed through optical filters170A-170C, and detected by optical detectors 160A-160C. Collectionoptics 112A-112C may each include one or more lenses made of glass,plastic, or other material that is optically transparent over apredetermined range of wavelengths. Collection optics 112A-112C mayinclude other optical devices or components including coating and/orlayers that may act as filters. For example, collection optics 112A mayinclude a coating that filters the light that passes through 112A toallow collection of light over a range of wavelengths corresponding toluminescent, fluorescent and/or phosphorescent light of the tags therebyeliminating, or augmenting, filter 170A. In some example embodiments,each of the filters 170A-170C may include more than one filter. Forexample, filter 170A may include two filters such that a portion of thelight from collection optics 112A passes through a first filter part of170A and a second portion may pass through a second filter part in 170A.Detectors 160A-160C may include one or more detectors. Continuing theprevious example, a first detector may be positioned to receive lightfrom the first filter part in 170A and a second detector may bepositioned to receive light from the second filter part in 170A. Thedetectors 160A-160C may detect luminescent light, fluorescent light,and/or phosphorescent light from the tags and biosamples in sample wells110A-110C.

The multiple sample wells 110A-110C may allow simultaneous, or nearsimultaneous, interrogation of different luminescent, fluorescent,and/or phosphorescent tags or species. One or more of the thermal layer,the sample wells, collection optics, filters, and detectors may includealignment pins to provide for self-registration of one layer to another.In some example embodiments, the bioassay system may withstand largeoperating temperature swings such as between 100 degrees Celsius and 3degrees Celsius. Other temperature swings may also be used.

FIG. 2 depicts an example of a bioassay system 200 showing exampledimensions and materials, in accordance with some example embodiments.The description of FIG. 2 also references some of the components thatwere discussed in FIG. 1. FIG. 2 includes five sample wells rather thanthe three sample wells of FIG. 1. Bioassay system 200 includes thermallayer 130, sample wells 112A-110E, optical substrate 210, collectionoptics 112A-112E, filters 170 and detectors 160.

In the example of FIG. 2, sample wells 110A-110E are included as part ofthermal layer 130. Sample wells 110A-110E may be made from the samematerial as thermal layer 130 such as copper or other material.

In the example of FIG. 2, optical substrate 210 may distribute andinject light into sample wells 110A-110E, collect any emittedluminescent, fluorescent, or phosphorescent light, and direct theemitted light toward the filters 170 and detection layer 160 includingdetectors 160A-160E. Detection layer 160 may include one or moredetection circuits coupled to detectors 160A-160E. In some exampleembodiments, detection layer 160 may be combined with filter layer 170.In some example embodiments, filter layer 170 may include thin-filmcolor filters coupled to detection layer 160. Detection layer 160 mayinclude an array of large area photodetectors such as photodiodes. Inother example embodiments, filter layer 170 may include a diffractiongrating and the detection layer may include a two-dimensional array ofcharge coupled or complementary metal oxide semiconductor (CMOS)detectors.

In some example embodiments, large core multimode fibers may be usedthat have a high contrast index of refraction between the cladding andcore, and high OH (hydroxyl ion) concentration. The foregoing featuresmay aid spectral probing of fluorescent or chemiluminescent samples. Theadvantages of large core multimode fibers include an efficient couplingto light-emitting diodes (LEDs), multi-mode support for multi-spectraloptical sources, and effective injection of light into sample wells.

Filtered LED sources used for optical source(s) 140 may producewavelengths of light that may cause fluorescence (of phosphorescence, orluminescence) of tags used in PCR. For example one optical source maycause fluorescence of tags and dyes such as fluorescein isothiocyanate(FITC), fluorescein (FAM), and/or others. In some example embodiments,an emission filter may be coupled to an LED source to narrow thelinewidth of the source and decrease the likelihood of crosstalk fromthe pump source light to the tag or dye generated optical signal. Theemission filter may be mounted in the LED housing or may be fibercoupled. As described above, and detailed below with respect to FIG. 3,fiber 142 from optical source(s) 140 may include a plurality ofoutcouplers 220A-220I placed at locations corresponding to nine samplewells (not shown in FIG. 3) similar to outcouplers 220A-220E placed atlocations corresponding to sample wells 110A-110E in FIG. 2. Eachoutcoupler 220A-220I may be implemented at least in-part by the removalof some cladding surrounding the fiber core at the locations where lightemission will illuminate each of the sample wells. Outcouplers may beplaced along the length of a fiber such as 142. For example, outcoupler220A may be the closest outcoupler to optical source(s) 140 andaccordingly the light intensity in fiber 142 is highest because no lighthas been coupled out before outcoupler 220A. Outcoupler 220A emits aportion of the light from optical source(s) 140 with the remainingportion passing further along fiber 142. The next outcoupler emits aportion of the remaining light propagating in fiber 142, and so on. Inthis way, each outcoupler emits a portion of the light propagating infiber 142. Accordingly, the optical power in fiber 142 is less at eachsuccessive outcoupler from 220A to 220E. To provide equal, or nearlyequal, optical power at each outcoupler 220A-220E, the pattern ofremoved cladding may be different at different locations to accommodatethe reduced optical power at each outcoupler. In some exampleembodiments, the core underneath the fiber cladding may be nicked orotherwise changed to enhance light emission as described further withrespect to FIG. 3.

The dimensions shown in FIG. 2 are example dimensions. In the example ofFIG. 2, the lens of collection optics 112A-112E is 4 millimeters indiameter and the spacing between sample wells 110A-110E is 5millimeters. The thermal layer 130 may be any metal or thermallyconductive material. In the example of FIG. 2, the thermal layer 130 andsample wells 110A-110E are shown as copper. In other embodiments, thethermal layer may be another metal or thermally conductive material andthe sample wells may be other material such as metal, thermallyconductive material, or other material such as a plastic.

FIG. 3 depicts an example of combining multiple optical sources andexamples of outcouplers, in accordance with some example embodiments.The description of FIG. 3 also references some of the components thatwere described in FIGS. 1-2. Each of multiple optical sources (e.g.,LEDs in FIG. 3) may be coupled to a different fiber. Each optical sourcemay produce light at a different wavelength or range of wavelengths. Thelight propagating in the multiple fibers may be combined and coupled toone optical fiber. The optical fiber may be routed in a bioassay systemto a plurality of sample wells. Cladding may be removed from the opticalfiber to cause emission of light from the optical fiber where thecladding is removed. The core may also be changed to enhance lightemission.

In the example of FIG. 3, optical source(s) 140 includes LED sources 310and 320. LED sources 310 and 320 may produce light over different bandsof wavelengths or the same band of wavelengths. LED source 310 iscoupled to fiber 316A, passed through filter 312, mode scrambler 314,and provided to combiner 330. LED source 320 is coupled to fiber 326A,passed through filter 322, mode scrambler 324, and provided to combiner330. LED sources 310 and 320 may be switched on and off and/or the drivecurrent adjusted as a function of time by controller 150. Filters 312and 322 may filter the LED outputs of LEDs 210 and 320 to reduce thelinewidth of the light passed to mode scramblers 314 and 324 and/or toreduce optical noise, interference, and/or cross-talk between lightsources. Filters 312 and 322 may pass different bands of wavelengths.Mode scramblers 314 and 324 induce mode coupling to provide a modaldistribution that is independent of the optical sources 310 and 320. Themode scrambled light is provided to combiner 330 via fibers 316 and 326.Combiner 330 may combine the light carried by fibers 316 and 326 andprovide the combined light to source fiber 142.

In some example embodiments, instead of source fiber 142 providing lightto optical splitter 120 and illuminators 114A-114C as shown in FIG. 1,source fiber 142 may have cladding around the core removed to createilluminators or outcouplers at locations corresponding to the samplewells. The bottom section of FIG. 3 depicts an example of thisconfiguration, where the source fiber 142 includes outcouplers 220A-220Iat illustrated positions similar to outcouplers 220A-220E in FIG. 2. Insome example embodiments, the core of the source fiber may be etched,scored, or material from the core otherwise removed to enhance theemission of light at the outcoupler. For example, source fiber 142 maybe machined or otherwise changed at outcoupling locations along thelength of the fiber to pump the samples at sample wells such as samplewells 110A-110C in FIG. 1. In some example embodiments, the outcouplerscause light emission across a broad range of wavelengths such as acrossthe visible electromagnetic spectrum or a broader range of wavelengths.By removing the cladding of fiber 142, light is emitted from sourcefiber 142 into the sample wells to cause pumping of the tags/dyes. Theamount of light exiting each outcoupler is adjustable by increasing thesize of the outcoupler, the area of the cladding removed, and/or thedepth of core removal.

The locations along source fiber 142 of the outcouplers such asoutcouplers 220A-220I in FIG. 3 may be aligned with the locations ofnine sample wells (not shown in FIG. 3 but similar to sample wells110A-110E in FIG. 2). In the example of FIG. 2, the locations ofoutcouplers 220A-220E are aligned with sample wells 110A-110E. In someexample embodiments, the cladding of fiber 142 and optionally the coremay be etched after source fiber 142 has been attached or affixed to anoptical substrate such as substrate 210 in FIG. 2. For example, sourcefiber 142 may be attached with epoxy glue into a machined recessmatching the diameter of source fiber 142. The cladding may beselectively removed using either masking and etching, a mechanicalmachining process, or by computer controlled laser ablation. Thelocations of the outcouplers may be controlled using alignment featuresmachined into the substrate 210. In some example embodiments, the sourcefiber may be coupled to a planar waveguide in optical substrate 210where outcouplers are created. Planar waveguide structures may includesilicon dioxide on silica, photo sensitive polymer waveguides, orinjection molding. In some example embodiments, the optical substrate210 may be machined to include alignment pins, vertical standoffs,recesses for collection optics, and troughs for waveguide and/or sourcefiber registration.

As described above, as light travels down source fiber 142, the light isattenuated by the successive outcouplers. Accordingly, the lightprovided to the “downstream” wells (closer to the end of source fiber142 at the last sample well) to have lower optical intensity thanupstream outcouplers. The amount of cladding removed at the successiveoutcouplers may be adjusted to compensate for this reduced lightintensity to cause a nearly uniform light emission at each outcoupleralong the source fiber 142. In other embodiments, the pattern of thecladding removal at the outcouplers may be uniform but the depth of anetching into the cladding may be different. In other embodiments, thepattern of cladding removal and the etch depth may be the same or nearlythe same, but a surface coating may be applied to inhibit light emissionout of the source fiber 142 into one or more sample wells.

FIG. 4 depicts an example of collection optics, in accordance with someexample embodiments. The description of FIG. 4 also references some ofthe components described in FIGS. 1-3. In some example embodiments suchas the bioassay system in FIG. 2, substrate 210 may be machined toregister and hold in place one or more optical devices for collectionoptics such as collection optics 112A-112E. The collection optics maycouple light from sample wells 110A-110E into optical filters 170 anddetectors 160. For example, each collection optics 112A-112E may includea lens such as the example lens shown in FIG. 4. Light generated in thesample wells 110A-110E may radiate omni-directionally. In some exampleembodiments, the thermal layer 130 and/or sample wells 110A-110E in FIG.2 may be reflective. For example, the sample wells may be made from areflective material or metallic or reflective inserts may be included toreflect light from the edges of the sample well toward the top surfaceand collection optics for each sample well. The light may propagatethrough the optical substrate 210 and may be collected by the collectionoptics 112A-112E. In some example embodiments, a portion of the lightreflected from each sample well may be blocked by the source fiber 142and outcouplers, but because the source fiber has a small area comparedto the to the area of the top surface of each sample well, theproportion of the emitted light that is blocked is insignificant. Insome example embodiments, optical substrate 210 may be machined toaccept, align, and/or self-register collection optics 112 including lens112A. The machining may hold a lens such as lens 112A at a position toimage a sample well onto an optical detector. As used above, machiningmay include one or more of machining via mechanical devices, chemicalmachining, etching, photolithography, or any other method of selectivelycausing material to be removed from a substrate such as opticalsubstrate 210. In some example embodiments, the optical substrate,alignment features, recesses, and/or lens, may be fabricated using arapid prototyping and/or injection molding.

FIG. 4 depicts some example sizes and distances. In the example of FIG.4, the lens as part of collection optics 112A has clear aperture of 4.8millimeters, the thickness is 3.02 millimeters, and the lens has a focallength of 2.37 millimeters. Other sizes, distances, and focal lengthsmay also be used.

FIG. 5 depicts an example of a plot of wavelength vs. optical densityfor an example optical filter, in accordance with some exampleembodiments. Example plot 500 plots wavelength in nanometers versesoptical density for a particular optical filter such as one or more ofoptical filters 170A-170C in FIG. 1. The plotted transmissivity curve530 shows a peak optical density between approximately 510 nanometersand 580 nanometers. The transmissivity plot shown in FIG. 5 isillustrative. Other transmissivity characteristics may also be used.Filters consistent with the disclosed subject matter may have wider ornarrower linewidths and may be centered at longer or shorter wavelengthsthan depicted in FIG. 5.

FIG. 6 depicts an example of bioassays with two optical filters and twodetectors per bioassay, in accordance with some example embodiments. Thedescription of FIG. 6 also references some of the components describedin FIGS. 1-5. FIG. 6 depicts a thermal layer 130 including, or coupledto, sample wells 110A and 110B, optical substrate 210 coupled to thermallayer 130 and collection optics 112A and 112B. Source fiber includingoutcouplers (not shown) may be placed to emit light into sample wells110A and 110B. Collection optics 112A and 112B focus luminescent,phosphorescent, and/or fluorescent light onto detectors 610A-610B and612A-612B from the tags and biosamples in sample wells 110A-110B.

In the example of FIG. 6, collection optics 112A is aligned to focuslight on detectors 610A and 610B. Between the collection optics 112A anddetectors 610A-610B are filters 620A-620B. Filter 620A is aligned to beilluminated by half or another portion of the light from collectionoptics 1112A. Filter 610B is aligned to be illuminated by the other halfor another portion of the light from collection optics 112A. The lightincident on detector 610A passes through filter 620A and the light ondetector 610B passes through filter 620B. Collection optics 112B isaligned to direct the light through filter 620B and 620C to illuminatedetectors 612A and 612B in a similar fashion. In this way, light frommultiple tags or dyes may detected from one sample well at the same timeor nearly the same time without changing samples, sources or filters.

The bioassays shown in FIG. 6 enable detection of light from multipletags at the same time or nearly the same time. The sample wells such as112A and 112B may be pumped by multiple wavelengths corresponding tomultiple tags at the same time. In the example of FIG. 6, each of twotags at each well location may be pumped by a source producing apredetermined wavelength. Light from both sources may be carried by asource fiber and emitted into sample wells 110A-10B. A first tag may bepumped by the first wavelength carried by the source fiber, and a secondtag may be pumped by the second source carried by the source fiber. Thefirst tag may generate luminescent, phosphorescent, and/or fluorescentlight that passes through 620A but not through filter 620B and isdetected by detector 610A. The second tag may generate luminescent,phosphorescent, and/or fluorescent light that passes through 620B butnot through filter 620A, and is detected by detector 610B.

A detection layer such as detection layer 160 included in FIG. 6 mayinclude detectors 610A-610B and 612A-612B, and detection circuit 605.Detectors 610A-610B and 612A-612B may include an array of photodetectorsmounted to a surface. For example, photo detectors may be located on acircuit board of the detection circuit 605 and aligned to be in positionto receive light as described above. The circuit board may includeon-board low-noise amplifiers and/or other electronics. In the exampleof FIG. 6, each sample well location includes two photodetectors tosample the light from two tags. In some example embodiments, the twolight sources that produce the two different pump wavelengths may bepulsed at the same time or at different times. Pulsing of the lightsources, such as pulsing the sources at different times or at differentfrequencies may facilitate electronic filtering and cross-talkreduction. Lock-in techniques may reduce noise and/or interference. Insome implementations, when a sample well contains two tags, each tag maybe pumped and/or a corresponding detector read at different times.

In some example embodiments, one or more diffraction gratings mayreplace one or more of the filters. A diffraction grating may separatecolors with no, or little, attenuation of light intensity. A diffractiongrating may reduce backscatter of rejected light. A diffraction gratingmay have a predetermined number of grating lines per unit length and mayhave a certain thickness. For example, a diffraction grating may have1200 lines per millimeter and be 3 millimeters thick. In some exampleembodiments, a diffraction grating with 1200 lines per millimeter mayprovide spectral dispersion to allow a linear or two-dimensional arrayof detectors to separate the light from tags and to discriminate againstany unconverted pump light reaching the detectors. Diffraction gratingsmay provide good sensitivity due to their low insertion loss, backgroundrejection, pump segregation, fluctuation removal, and stable fluorescentdye characterization.

FIG. 7 depicts an example set of parameter values associated with adiffraction grating configuration that uses various dyes, in accordancewith some example embodiments. The example diffraction grating has 1200lines per millimeter. FIG. 7 includes six fluorescent dyes as examples.Other dyes may be used as well. The disclosed subject matter supportsany dye.

The dyes included in FIG. 7 include: CF 1 at 710A, FAM at 710B, AlexaFluor 532 at 710C, Texas Red at 710D, Alexa Fluor 647 at 710E, and CF 6at 710F. The table shown in FIG. 7 shows two columns for each dyeincluding minimum and maximum emission wavelengths. The grating equation780 may be used to calculate the first order diffracted angle. Thegrating equation may then be solved to obtain a single stand-offdistance “Separation (t) Grating to Detector (mm)” of 8.9 mm at 740.This distance may be chosen to give a dispersion distance to allow alinear detector array to have a sufficient number of non-overlappingpixels for detection of the individual emission wavelengths of theselected dyes.

The calculation of the “x distance from Normal (mm)” at 750 is thelinear distance at the detector plane (a plane made by the top surfacesof the detectors at 160) illuminated by a specific dye. The differencebetween the high and low wavelength locations on the detector plane isused to calculate the “Detector width at offset t (mm)” at 760. Theadjacent column illustrates the number of illuminated pixels when a 12mm linear detector array is used with 512 pixels. Illuminated pixelsshown in row 760 indicate that the FAM tag has the minimum number ofadjacent active pixels at 24 pixels for the 8.9 mm standoff.

A one-dimensional array or a two-dimensional array may processelectrical signals from the individual pixels. For example, theprocessing may sum the appropriate detector signals, gate the detectorsignals in time using lock-in techniques, and time average the signalsto reduce noise. The “image” of the sample may be a “spectral spread”with each region being indicative of an individual light signature froma tag. The second dimension of the detector array may allow additionalparallel rows of sample wells.

The foregoing large area detector and diffraction grating may betolerant of some optical issues that may occur in the propagation path.For example, the pump light that reflects back into the detector planemay be at a different spatial location than the generated fluorescentlight. Also, ineffective collimation at the collection optics maybroaden the receive spot as rays impinge upon the diffraction grating atdifferent angles.

Automated calibration and background rejection schemes can beaccommodated by using the pump, diffraction, and detector plane duringperiods when the temperature and resulting chain reactions are notactive. For example, off-cycle calibrations of the pump light locationand intensity can be measured.

Furthermore, for cyclic processes such as PCR amplification monitoring,fluorescence fluctuations can be removed by n-cycle moving averagecomputation from cycle to cycle to smooth out fluctuations and noisewithin individual wells cycle to cycle. The emitted signal in PCR may beexponential. Once the signal passes above a threshold of a detector,fluctuations become less of an issue in terms of assessing targetpresence and concentration via qPCR analysis.

Offsets or errors due to well-to-well variability and variability ofsample well alignment may be reduced using background subtraction andnormalization for each well to enable repeatable and accuratefluorescence intensity change measurements using standard normalizationand background subtraction techniques.

FIG. 8 depicts an example of a process for processing a plurality ofbiosamples, in accordance with some example embodiments. At 810, a firstsample well from a plurality of sample wells contains a biosample andone or more reagents. At 820, the plurality of sample wells are heated.At 830, an optical substrate layer coupled to the thermal layer and thesample wells distributes light from a source fiber to each of the samplewells. At 840, one or more filters coupled to the substrate layerfilters light generated by the one or more reagents in response to theexcitation. At 850, one or more detectors coupled to the opticalsubstrate at the first sample well detect light emitted from the assayin the first sample well.

At 810, a first sample well such as sample well 110A may contain abiosample and one or more reagents. For example, the sample well maycontain a biosample including DNA and one, two, three, or any othernumber of tags. The first sample well may be one of a plurality ofsample wells such as sample wells 110A-110C in FIG. 1. Each sample wellmay include a different assay. For example, sample well 110B may containa different biosample and/or different tags from sample well 110A. Thefirst sample well includes a first assay.

At 820, the plurality of sample wells such as sample wells 110A-110C inFIG. 1 may be heated by a planar heater such as thermal layer 130. Theplanar heater may be coupled to the plurality of sample wells. Forexample, FIG. 1 depicts sample wells 110A-110C coupled to thermal layer130.

At 830, an optical substrate layer such as optical substrate layer 210in FIG. 2 may be coupled to sample wells 110A-110E. The opticalsubstrate layer may include a source fiber such as source fiber 142 withoutcouplers at the locations of the sample wells described above. One ormore wavelengths of light may propagate in source fiber 142 as describedabove with respect to FIG. 3. Cladding may be removed and the coremachined at the outcouplers in source fiber 142 as describe above. Lightmay be emitted at the outcouplers to provide excitation to the assayssuch as the first assay in the first sample well.

At 840, one or more filters coupled to the substrate layer, filter lightgenerated by the one or more reagents in response to the excitation. Forexample, FIG. 6 shows filters 610A and 610B filtering light from opticalsubstrate 210 and sample well 110A.

At 850, each sample well may have one or more associated detectors. Forexample, in FIG. 6 detectors 610A and 610B are associated with samplewell 110A and detectors 612A and 612B are associated with sample well110B. The detectors may be coupled to the filters such as filters 620Aand 620B, and/or the detectors may be coupled to detection circuit 605.Light emitted from the reagents or tags in the first assay in the firstsample well 110A may be collected by collection optics 112A, filtered byfilters 620A and 620B, and provided to detectors 610A and 610B.

The subject matter described herein may be embodied in systems,apparatus, methods, and/or articles depending on the desiredconfiguration. For example, the systems, apparatus, methods, and/orarticles described herein can be implemented using one or more of thefollowing: materials such as silica, glass, metals, or any othermechanical material, electronic components such as transistors,inductors, capacitors, resistors, and the like, a processor executingprogram code, an application-specific integrated circuit (ASIC), adigital signal processor (DSP), an embedded processor, a fieldprogrammable gate array (FPGA), and/or combinations thereof. Thesevarious example embodiments may include implementations in one or morecomputer programs that are executable and/or interpretable on aprogrammable system including at least one programmable processor, whichmay be special or general purpose, coupled to receive data andinstructions from, and to transmit data and instructions to, a storagesystem, at least one input device, and at least one output device. Thesecomputer programs (also known as programs, software, softwareapplications, applications, components, program code, or code) includemachine instructions for a programmable processor, and may beimplemented in a high-level procedural and/or object-orientedprogramming language, and/or in assembly/machine language. As usedherein, the term “machine-readable medium” refers to any computerprogram product, computer-readable medium, computer-readable storagemedium, apparatus and/or device (for example, magnetic discs, opticaldisks, memory, Programmable Logic Devices (PLDs)) used to providemachine instructions and/or data to a programmable processor, includinga machine-readable medium that receives machine instructions. In thecontext of this document, a “machine-readable medium” may be anynon-transitory media that can contain, store, communicate, propagate ortransport the instructions for use by or in connection with aninstruction execution system, apparatus, or device, such as a computeror data processor circuitry. A computer-readable medium may comprise anon-transitory computer-readable storage medium that may be any mediathat can contain or store the instructions for use by or in connectionwith an instruction execution system, apparatus, or device, such as acomputer. Furthermore, some of the embodiments disclosed herein includecomputer programs configured to cause methods as disclosed herein (see,for example, controller 150 in FIG. 1 and/or the process 800 in FIG. 8).

Although a few variations have been described in detail above, othermodifications or additions are possible. In particular, further featuresand/or variations may be provided in addition to those set forth herein.Moreover, the example embodiments described above may be directed tovarious combinations and subcombinations of the disclosed featuresand/or combinations and subcombinations of several further featuresdisclosed above. In addition, the logic flow depicted in theaccompanying figures and/or described herein does not require theparticular order shown, or sequential order, to achieve desirableresults. Other embodiments may be within the scope of the followingclaims.

Similarly, while operations are depicted in the drawings in a particularorder, this should not be understood as requiring that such operationsbe performed in the particular order shown or in sequential order, orthat all illustrated operations be performed, to achieve desirableresults. Moreover, the separation of various system components in theembodiments described in this patent document should not be understoodas requiring such separation in all embodiments.

Only a few implementations and examples are described and otherimplementations, enhancements and variations can be made based on whatis described and illustrated in this patent document.

What is claimed is:
 1. A planar biochemical device, the devicecomprising: a plurality of sample holders arranged in a planarconfiguration forming a one-dimensional or a two-dimensional array, eachsample holder configured for an assay comprising one or more biosamplesand one or more reagents; a planar heater coupled to the plurality ofsample holders, wherein the planar heater is operable to heat theplurality of sample holders; an optical substrate layer coupled to theplurality of sample holders; one or more optical sources to providelight to each of the sample holders, wherein a first optical source ofthe one or more optical sources comprises a light source and a modescrambler producing an optical modal distribution that is independent ofthe light source; an optical fiber configured to transmit light from theone or more optical sources to the optical substrate layer, wherein theoptical fiber is further configured to couple light to one or more ofthe plurality of sample holders through openings in a cladding of theoptical fiber at a plurality of predetermined locations; and an opticaldetection layer positioned to receive an input light from the pluralityof sample holders, the optical detection layer including a plurality ofoptical detectors in alignment with the plurality of sample holders todetect the input light.
 2. The planar biochemical device of claim 1,further comprising: one or more optical filters positioned between theoptical detection layer and the optical substrate layer, wherein eachoptical filter passes light of a predetermined wavelength and passbandand rejects light outside the predetermined wavelength and passband. 3.The planar biochemical device of claim 1, further comprising: one ormore diffraction gratings positioned between the optical detection layerand the optical substrate layer, each diffraction grating configured toseparate different colors of the input light with little or noattenuation, and wherein the optical detection layer includes atwo-dimensional array of charge-coupled optical detectors, or atwo-dimensional array of complementary metal oxide semiconductor opticaldetectors.
 4. The planar biochemical device of claim 1, wherein theopenings in the cladding of the optical fiber are outcouplers and theplurality of predetermined locations correspond to the plurality ofsample holders.
 5. The planar biochemical device of claim 1, wherein theoptical substrate layer distributes light having at least two differentranges of wavelengths.
 6. The planar biochemical device of claim 1,wherein the optical detection layer is configured to produce a responseto one or more of luminescent light, fluorescent light, orphosphorescent light.
 7. The planar biochemical device of claim 1,wherein the optical substrate layer comprises one or more lensespositioned between the one or more sample holders and the opticaldetection layer, wherein the one or more lenses are aligned orself-registered with the plurality of sample holders.
 8. The planarbiochemical device of claim 1, wherein the openings in the cladding havedifferent sizes at at least two of the plurality of predeterminedlocations to allow different amounts light to be emitted towards atleast two of the sample holders.
 9. A planar biochemical device, thedevice comprising: a plurality of sample holders arranged in a planarconfiguration forming a one-dimensional or a two-dimensional array, eachsample holder configured for an assay comprising one or more biosamplesand one or more reagents; a planar heater coupled to the plurality ofsample holders, wherein the planar heater is operable to heat theplurality of sample holders; an optical substrate layer coupled to theplurality of sample holders wherein the optical substrate layercomprises a plurality of lenses positioned between the plurality ofsample holders and the optical detection layer, wherein the plurality oflenses are aligned or self-registered with the plurality of sampleholders; one or more optical sources to provide light to each of thesample holders, wherein a first optical source of the one or moreoptical sources comprises a light source and a mode scrambler producingan optical modal distribution that is independent of the light source;and an optical detection layer positioned to receive an input light fromthe plurality of sample holders, the optical detection layer including aplurality of optical detectors in alignment with the plurality of sampleholders to detect the input light.